All Stories

  1. Survey of metaproteomics software tools for functional microbiome analysis

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  2. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

    Article • GigaScience, December 2019, Oxford University Press (OUP)

    Björn Grüning

  3. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

    Article • GigaScience, December 2019, Oxford University Press (OUP)

    Dr Oliver Schilling, Björn Grüning

  4. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

    Article • F1000Research, November 2019, Faculty of 1000, Ltd.

    Björn Grüning

  5. The RNA workbench 2.0: next generation RNA data analysis

    Article • Nucleic Acids Research, May 2019, Oxford University Press (OUP)

    Björn Grüning

  6. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Oliver Schilling, Björn Grüning

  7. Software engineering for scientific big data analysis

    Article • GigaScience, May 2019, Oxford University Press (OUP)

    Björn Grüning

  8. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  9. Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Björn Grüning

  10. Pou5f3, SoxB1, and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation

    Article • Genome Research, January 2019, Cold Spring Harbor Laboratory Press

    Björn Grüning

  11. Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells

    Article • Experimental Eye Research, January 2019, Elsevier

    Björn Grüning

  12. Update on the moFF Algorithm for Label-Free Quantitative Proteomics

    Article • Journal of Proteome Research, December 2018, American Chemical Society (ACS)

    Björn Grüning

  13. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Björn Grüning, Susheel Varma, Pablo Moreno, Dr. Yasset Perez-Riverol

  14. Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Björn Grüning

  15. Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Björn Grüning

  16. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

    Article • Nucleic Acids Research, May 2018, Oxford University Press (OUP)

    Björn Grüning

  17. High-resolution TADs reveal DNA sequences underlying genome organization in flies

    Article • Nature Communications, January 2018, Nature

    Björn Grüning

  18. ENASearch: A Python library for interacting with ENA's API

    Article • The Journal of Open Source Software, October 2017, The Open Journal

    Björn Grüning

  19. Practical computational reproducibility in the life sciences

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Björn Grüning

  20. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

    Article • PLoS Pathogens, October 2017, PLOS

    Björn Grüning

  21. Recent advances in RNA folding

    Article • Journal of Biotechnology, July 2017, Elsevier

    Björn Grüning

  22. Four simple recommendations to encourage best practices in research software

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Dr Monther Alhamdoosh, Mr Rafael C Jimenez, Mr Neil P Chue Hong, Professor Josep Ll. Gelpi, Prof Carole A Goble, Rob Hooft, Daniel S Katz, Mr Federico López Gómez, Dr Sonika Tyagi, Sonika Tyagi, Mateusz Kuzak, Allegra Via, Xiaochuan (Harry) Wang, Montserrat Gonzalez, Björn Grüning, Andrew Treloar, Nathan Watson-Haigh, Dr. Yasset Perez-Riverol

  23. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

    Article • Nucleic Acids Research, June 2017, Oxford University Press (OUP)

    Björn Grüning, Altuna A

  24. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

    Article • PLoS Computational Biology, May 2017, PLOS

    Björn Grüning

  25. RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

    Article • Journal of Biotechnology, May 2017, Elsevier

    Björn Grüning

  26. ReGaTE: Registration of Galaxy Tools in Elixir

    Article • GigaScience, April 2017, Oxford University Press (OUP)

    Björn Grüning, Matúš Kalaš

  27. BioContainers: an open-source and community-driven framework for software standardization

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  28. GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders

    Article • Genetics Research, January 2017, Cambridge University Press

    Tobias Hornig, Björn Grüning

  29. 5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

    Article • PLoS ONE, November 2016, PLOS

    Björn Grüning

  30. PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

    Article • PLoS ONE, October 2016, PLOS

    Björn Grüning

  31. Enhancing pre-defined workflows withad hocanalytics using Galaxy, Docker and Jupyter

    Article • September 2016, Cold Spring Harbor Laboratory Press

    Björn Grüning

  32. Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster

    Article • BMC Genomics, August 2016, Springer Science + Business Media

    Björn Grüning

  33. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

    Article • Nucleic Acids Research, May 2016, Oxford University Press (OUP)

    Björn Grüning

  34. deepTools2: a next generation web server for deep-sequencing data analysis

    Article • Nucleic Acids Research, April 2016, Oxford University Press (OUP)

    Björn Grüning

  35. MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing

    Article • Investigative Ophthalmology & Visual Science, April 2016, Association for Research in Vision and Ophthalmology (ARVO)

    Björn Grüning

  36. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

    Article • Cancer Informatics, April 2016, Libertas Academica, Ltd.

    Björn Grüning

  37. Tools and data services registry: a community effort to document bioinformatics resources

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Björn Grüning, Dr Tunca Dogan, Matúš Kalaš

  38. DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro

    Article • Stem Cells, September 2015, Wiley

    Björn Grüning

  39. NCBI BLAST+ integrated into Galaxy

    Article • GigaScience, August 2015, Oxford University Press (OUP)

    Björn Grüning

  40. Anatomy of BioJS, an open source community for the life sciences

    Article • eLife, July 2015, eLife

    Mr Bruno Vieira, Björn Grüning, Saket Choudhary

  41. Deciphering the Epigenetic Code of Cardiac Myocyte TranscriptionNovelty and Significance

    Article • Circulation Research, June 2015, Wolters Kluwer Health

    Björn Grüning

  42. The Purchasable Chemical Space: A Detailed Picture

    Article • Journal of Chemical Information and Computer Sciences, May 2015, American Chemical Society (ACS)

    Björn Grüning

  43. NCBI BLAST+ integrated into Galaxy

    Article • January 2015, Cold Spring Harbor Laboratory Press

    Björn Grüning

  44. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

    Article • Nature Communications, October 2014, Nature

    Björn Grüning

  45. Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

    Article • Nature Medicine, October 2014, Nature

    Björn Grüning

  46. PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering

    Article • Bioinformatics, July 2014, Oxford University Press (OUP)

    Björn Grüning

  47. deepTools: a flexible platform for exploring deep-sequencing data

    Article • Nucleic Acids Research, May 2014, Oxford University Press (OUP)

    Björn Grüning

  48. Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling inStreptomyces

    Article • Journal of the American Chemical Society, April 2014, American Chemical Society (ACS)

    Björn Grüning

  49. Dynamic information system for small molecules

    Article • Journal of Cheminformatics, January 2014, Springer Science + Business Media

    Björn Grüning

  50. ChemicalToolBoX and its application on the study of the drug like and purchasable space

    Article • Journal of Cheminformatics, January 2014, Springer Science + Business Media

    Björn Grüning

  51. Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Glarea lozoyensis Indicates High Diversity within the Order Helotiales

    Article • PLoS ONE, September 2013, PLOS

    Björn Grüning

  52. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

    Article • PeerJ, September 2013, PeerJ

    Björn Grüning

  53. Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of Avilamycin

    Article • Genome Announcements, June 2013, ASM Journals

    Björn Grüning

  54. StreptomeDB: a resource for natural compounds isolated from Streptomyces species

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    Björn Grüning

  55. Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family

    Article • Eukaryotic Cell, February 2012, ASM Journals

    Björn Grüning

  56. Mining and evaluation of molecular relationships in literature

    Article • Bioinformatics, January 2012, Oxford University Press (OUP)

    Björn Grüning

  57. Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

    Article • Nature Methods, November 2011, Nature

    Björn Grüning

  58. Genome Sequence of Streptomyces sp. Strain Tu6071

    Article • Journal of Bacteriology, June 2011, ASM Journals

    Björn Grüning

  59. Compounds In Literature (CIL): screening for compounds and relatives in PubMed

    Article • Bioinformatics, March 2011, Oxford University Press (OUP)

    Björn Grüning

  60. RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils

    Article • Nucleic Acids Research, May 2009, Oxford University Press (OUP)

    Björn Grüning

  61. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

    Article • Nucleic Acids Research, May 2009, Oxford University Press (OUP)

    Björn Grüning

  62. SuperScent--a database of flavors and scents

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning

  63. SuperToxic: a comprehensive database of toxic compounds

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning

  64. Voronoia: analyzing packing in protein structures

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning